Analyte detection cartridge and methods of use thereof

Abstract

Provided herein are devices (e.g., cartridges), instruments, systems, and components thereof for rapid sample processing and analyte detection (e.g., nucleic acid purification, amplification, and/or detection), and methods of use thereof. A cartridge for analyte detection may comprise: a storage section including a storage chamber; a processing section including a processing chamber; a microfluids section in fluid communication with the processing section; and a transfer capsule configured to transfer fluid between the storage chamber and the processing chamber

1 . A cartridge for analyte detection comprising:
 a storage section including a storage chamber;   a processing section including a processing chamber;   a microfluids section in fluid communication with the processing section; and a transfer capsule configured to transfer fluid between the storage chamber and the processing chamber.   
     
     
         2 . The cartridge of  claim 1 , wherein the processing section is positioned between the storage section and the microfluidic section. 
     
     
         3 . The cartridge of  claim 1 or 2 , further including a docking section with a access port in fluid communication with the storage chamber and a processing access port in fluid communication with the processing chamber. 
     
     
         4 . The cartridge of one of  claims 1-3 , further including a body that forms at least a portion of the storage section, at least a portion of the processing section, and at least a portion of the docking section. 
     
     
         5 . The cartridge of one of  claims 1-3 , wherein a first channel fluidly connects the storage access port and the storage chamber, and a second channel fluidly connects the processing access port and the processing chamber. 
     
     
         6 . The cartridge of one of  claims 1-5 , wherein the storage chamber includes a first end and a second end opposite the first end, the first end is positioned closer to the storage access port than the second end, and wherein the first channel connects to the storage chamber at the second end. 
     
     
         7 . The cartridge of one of  claims 1-5 , wherein the processing chamber includes a first end and second end opposite the first end, the first end is positioned closer to the processing access port than the second end, and wherein the second channel connects to the processing chamber at the second end. 
     
     
         8 . The cartridge of one of  claims 1-7 , wherein the storage chamber is a first storage chamber and the storage section further includes a second storage chamber. 
     
     
         9 . The cartridge of one of  claims 1-8 , wherein the processing chamber is a first processing chamber and the processing section further includes a second processing chamber. 
     
     
         10 . The cartridge of one of  claims 1-9 , wherein the storage section includes a cavity configured to receive the transfer capsule. 
     
     
         11 . The cartridge of one of  claims 1-10 , further including a first vent fluidly coupled to the storage chamber, and a second vent fluidly coupled to the processing chamber. 
     
     
         12 . The cartridge of one of  claims 1-11 , wherein the microfluids section includes a reaction chamber, a microfluidic vent channel fluidly connected to the reaction chamber, and a microfluidic inlet channel fluidly connecting the processing chamber and the reaction chamber. 
     
     
         13 . The cartridge of  claim 12 , wherein the microfluids section further includes a wax seal. 
     
     
         14 . The cartridge of  claim 13 , wherein the wax seal is a first wax seal and the microfluids section further includes a second wax seal, wherein the first wax seal is positioned adjacent the microfluidic inlet channel and the second wax seal is positioned adjacent the microfluidic vent channel. 
     
     
         15 . The cartridge of  claim 14 , wherein the second wax seal is positioned a distance from the reaction chamber, wherein the distance is at least 2 mm. 
     
     
         16 . The cartridge of  claim 12 , further including an offset vent channel fluidly connected to the microfluidic inlet channel. 
     
     
         17 . The cartridge of  claim 16 , wherein the offset vent channel is a first offset vent channel and the cartridge further includes a second offset vent channel fluidly connecting the first offset vent channel and the second vent. 
     
     
         18 . A microfluidic device comprising:
 (i) a reaction chamber,   (ii) an inlet channel in fluid communication with the reaction chamber;   (iii) a vent channel in fluid communication with the reaction chamber;   (iv) a first wax seal positioned adjacent to and in fluid communication with the inlet channel, wherein when first the wax seal is in a first position it does not occlude the inlet channel and allows fluid to enter the reaction chamber through the inlet channel, and wherein when first the wax seal is in a second position the first wax seal occludes the inlet channel and prevents fluid from entering or escaping the reaction chamber through the inlet channel;   (v) a second wax seal positioned adjacent to and in fluid communication with the vent channel, wherein when second the wax seal is in a first position it does not occlude the vent channel and allows gas to exit the reaction chamber through the vent channel, and wherein when second the wax seal is in a second position the second wax seal occludes the vent channel and prevents fluid from entering or escaping the reaction chamber through the vent channel;   wherein liquid reagents can be introduced to the reaction chamber through the inlet channel; and   wherein heating the wax seals above a threshold temperature melts the wax seals and subsequently cooling the wax seals below the threshold temperature solidifies the wax seals in the second position.   
     
     
         19 . A system comprising a cartridge of one of  claims 1-17  and an instrument into which the cartridge can be inserted, wherein the instrument comprises components to impart heating, magnetic transfer, fluid transfer, and/or analyte detection functionalities onto the cartridge. 
     
     
         20 . Use of a system of  claim 19  for sample processing and analyte detection. 
     
     
         21 . A microfluidic system comprising an inlet channel, a vent channel, and a reaction chamber; wherein the inlet channel is in fluid communication with the reaction chamber, wherein the vent channel is in fluid communication with the reaction chamber;
 the system further comprising a heating element capable of raising the temperature of the reaction chamber;   the system further comprising a first seal positioned adjacent to and in fluid communication with the inlet channel, wherein when first the seal is in a first position it does not occlude the inlet channel and allows fluid to enter the reaction chamber through the inlet channel, and wherein when the first seal is in a second position the first seal occludes the inlet channel and prevents fluid from entering or escaping the reaction chamber through the inlet channel;   the system further comprising a second seal positioned adjacent to and in fluid communication with the vent channel, wherein when the second seal is in a first position it does not occlude the vent channel and allows gas to exit the reaction chamber through the vent channel, and wherein when the second seal is in a second position the second seal occludes the vent channel and prevents fluid from entering or escaping the reaction chamber through the vent channel; and   wherein heating the seals above a threshold temperature melts the seals and allows the seals to flow from the first positions into the second positions, and wherein subsequently cooling the seals below the threshold temperature solidifies the wax seals in the second position.   
     
     
         22 . The system of  claim 21  wherein the first seal and the second seal comprise a wax or polymeric material. 
     
     
         23 . A heat transfer device for heating and cooling a reaction chamber, the heat transfer device comprising:
 a heat reservoir including a base, a first bore, a second bore, and a heat exchanger extending from the base; the heat exchanger includes a planar surface configured to about the reaction chamber;   a heater positioned within the first bore; and   a temperature sensor positioned within the second bore.   
     
     
         24 . The heat transfer device of  claim 23 , wherein the first bore and the second bore are formed in the base. 
     
     
         25 . The heat transfer device of  claim 23 , wherein the heat exchanger is cylindrical. 
     
     
         26 . The heat transfer device of  claim 23 , wherein the heat reservoir is Aluminum. 
     
     
         27 . The heat transfer device of  claim 23 , wherein the heater is an electric resistive heater. 
     
     
         28 . The heat transfer device of  claim 23 , wherein the reaction chamber is a PCR reaction chamber. 
     
     
         29 . The heat transfer device of  claim 23 , further including a processor and a non-transitory memory including instructions that when executed by the processor performs closed-loop temperature control of the heat reservoir. 
     
     
         30 . An assembly comprising:
 a first support;   a second support movable with respect to the first support;   a first heat transfer device with a first planar surface, the first heat transfer device coupled to the first support;   a second heat transfer device with a second planar surface positioned opposite the first planar surface, the second heat transfer device coupled to the second support; wherein the first heat transfer device and the second heat transfer device are at a first temperature;   a third heat transfer device with a third planar surface, the third heat transfer device coupled to the first support;   a fourth heat transfer device with a fourth planar surface positioned opposite the third planar surface, the fourth heat transfer device coupled to the second support; wherein the third heat transfer device and the fourth heat transfer device are at a second temperature different than the first temperature.   
     
     
         31 . The assembly of  claim 30 , further including a fluorimeter coupled to the first support and positioned between the first heat transfer device and the third heat transfer device. 
     
     
         32 . The assembly of  claim 31 , further including a fifth heat transfer device with a fifth planar surface position opposite the fluorimeter, the fifth heat transfer device coupled to the second support and positioned between the second heat transfer device and the fourth heat transfer device. 
     
     
         33 . The assembly of  claim 30 , wherein the assembly is configured to receive a reaction chamber between the first planar surface and the second planar surface to bring the reaction chamber to the first temperature; and between the third planar surface and the fourth planar surface to bring the reaction chamber to the second temperature. 
     
     
         34 . The assembly of  claim 33 , wherein the reaction chamber is a PCR chamber. 
     
     
         35 . The assembly of  claim 33 , further comprising an actuator coupled to the second support and configured to move the second support along a clamp axis between a first position in which the first planar surface and the second planar surface are spaced apart by a first distance, and a second position in which the first planar surface and the second planar surface are spaced apart by a second distance, smaller than the first distance. 
     
     
         36 . The assembly  claim 35 , Wherein the second distance is within a range of 400 micrometers to 600 micrometers. 
     
     
         37 . The assembly of  claim 33 , wherein the actuator is a first actuator, and the assembly further includes a second actuator coupled to the first support and the second support, wherein the second actuator is configured to move the first support and the second support together along a translation axis. 
     
     
         38 . The assembly of  claim 37 , wherein the translation axis is normal to the clamp axis. 
     
     
         39 . The assembly of  claim 30 , wherein the first temperature is within a range of 80 degrees C. and 100 degrees C. 
     
     
         40 . The assembly of  claim 30 , wherein the second temperature is within a range of 50 degrees C. and 70 degrees C. 
     
     
         41 . A fluidic device comprising:
 a reaction chamber;   a channel in fluid communication with the reaction chamber; and   a wax seal, wherein when the wax seal is in a first position it does not occlude the channel and allows fluid to enter or exit the reaction chamber through the channel, and when the wax seal is in a second position the wax seal occludes the channel and prevents fluid from entering or escaping the reaction chamber through the channel;   wherein heating the wax seal above a threshold temperature melts the wax seal and subsequently cooling the wax seal below the threshold temperature solidifies the wax seals in the second position.   
     
     
         42 . The fluidic device of  claim 41 , wherein the reaction chamber is in fluid communication with an inlet channel; and the fluidic device further includes a vent channel in fluid communication with the reaction chamber. 
     
     
         43 . The fluidic device of  claim 42 , wherein the inlet channel wax seal is a first wax seal and the fluidic device further includes a second wax seal, wherein when second the wax seal is in a first position it does not occlude the vent channel and allows fluid to exit the reaction chamber through the vent channel, and when the second wax seal is in a second position the second wax seal occludes the vent channel and prevents fluid from entering or escaping the reaction chamber through the vent channel. 
     
     
         44 . The fluidic device of  claim 43 , wherein the first wax seal is positioned adjacent the inlet channel and the second wax seal is positioned adjacent the vent channel. 
     
     
         45 . The fluidic device of  claim 41 , further comprising a first high-temperature movable heater capable of being positioned within a range of the wax seal to heat the wax seal above the threshold temperature. 
     
     
         46 . The fluidic device of  claim 45 , further comprising a second low-temperature movable heater capable of being positioned within a range of the wax seal to cool the wax seal below the threshold temperature. 
     
     
         47 . The fluidic device of  claim 46 , wherein the diameter of the wax seal is less than the diameter of the first and second heaters. 
     
     
         48 . The fluidic device of  claim 41 , wherein the wax seal is coated in an adhesive. 
     
     
         49 . The fluidic device of  claim 48 , wherein the adhesive is an acrylic adhesive. 
     
     
         50 . The fluidic device of  claim 41 , wherein the first and second heaters are capable of being positioned at selected positions relative to the wax seal. 
     
     
         51 . The fluidic device of  claim 41 , wherein the second wax seal is positioned a distance from the reaction chamber, wherein the distance is at least 2 mm. 
     
     
         52 . The fluidic device of  claim 42 , wherein a plurality of liquid reagents can be introduced to the reaction chamber through the inlet channel. 
     
     
         53 . A fluorimeter comprising:
 a casing including a measurement aperture;   a first light source coupled to the casing along a first light source axis;   a second light source coupled to the casing along a second light source axis;   a third light source coupled to the casing along a third light source axis;   a fourth light source coupled to the casing along a fourth light source axis;   a first light detector coupled to the casing along a first detector axis;   a second light detector coupled to the casing along a second detector axis;   a third light detector coupled to the casing along a third detector axis;   a fourth light detector coupled to the casing along a fourth detector axis;   wherein the first light source axis, the second light source axis, the third light source axis, the fourth light source axis, the first detector axis, the second detector axis, the third detector axis, and the fourth detector axis intersect the measurement aperture.   
     
     
         54 . The fluorimeter of  claim 53 , wherein the circular measurement aperture defines a normal axis through its center and perpendicular to the plane of the measurement aperture. 
     
     
         55 . The fluorimeter of  claim 54 , wherein the normal axis, the first light source axis, the second light source axis, the third light source axis, the fourth light source axis, the first detector axis, the second detector axis, the third detector axis, and the fourth detector axis are not co-axial. 
     
     
         56 . The fluorimeter of  claim 54 , the first light source axis, the second light source axis, the third light source axis, the fourth light source axis, the first detector axis, the second detector axis, the third detector axis, and the fourth detector axis are positioned circumferentially around the normal axis. 
     
     
         57 . The fluorimeter of  claim 53 , wherein the first light source is positioned circumferentially adjacent to the first detector. 
     
     
         58 . The fluorimeter of  claim 53 , wherein the fluorimeter does not include a dichroic mirror or a beam splitter. 
     
     
         59 . The fluorimeter of  claim 53 , further comprising a processor and a non-transitory memory including instructions that, when executed by the processor, store 400 analog to digital readings by the first detector made over a 100 millisecond time period. 
     
     
         60 . The fluorimeter of  claim 53 , wherein the first light source emits a first excitation light along the first light source axis; and wherein the first excitation light is reflected at the measurement aperture away from the first light detector axis. 
     
     
         61 . The fluorimeter of  claim 53 , wherein the measurement aperture is configured to receive a sample; and wherein the first excitation light from the first light source has a first spectrum and the first light detector measures a first fluorescence of the sample in response to the first excitation light. 
     
     
         62 . The fluorimeter of  claim 61 , wherein a second excitation light from the second light source has a second spectrum and the second light detector measures a second fluorescence of the sample in response to the second excitation light. 
     
     
         63 . The fluorimeter of  claim 53 , wherein the measurement aperture is configured to align with a planar surface of a PCR chamber. 
     
     
         64 . The fluorimeter of  claim 53 , wherein the first detector includes a first lens, a filter, a second lens, and a solid-state detector. 
     
     
         65 . A nucleic acid quantification method comprising:
 (a) performing a multicycle amplification reaction on a sample suspected of containing a target nucleic acid in the presence of a detectable reporter to produce an amplification product;   (b) detecting a signal from the detectable reporter that correlates with the amount of detectable reporter incorporated into the amplification product after each cycle of the amplification reaction;   (c) identifying earliest cycle with a normalized increase in signal that is greater than a cutoff value;   (d) fit a linear equation to a plurality of signals from cycles earlier than the earliest cycle with a normalized increase in signal that is greater than the threshold value;   (e) fit a curve to a plurality of signals from cycles later than the earliest cycle with a normalized increase in signal that is greater than the threshold value;   (f) identify the cycle (Cq) for which the normalized difference in signal for the linear equation and the curve is equal to a threshold value;   wherein Cq is inversely proportional to the amount of target nucleic acid present in the sample.   
     
     
         66 . The method of  claim 65 , wherein step (c) comprises:
 (i) identifying the cycle with the maximum normalized increase in signal;   (ii) if the maximum normalized increase in signal is greater than the cutoff value, then determine the earliest cycle prior to the cycle with the maximum normalized increase in signal that has a normalized increase in signal that is greater than a lower cutoff value.   
     
     
         67 . The method of  claim 65 , further comprising a step of calculating a moving average of the detected signal for each cycle of the amplification reaction and using the moving averages for each cycle for steps (c)-(f). 
     
     
         68 . The method of  claim 67 , wherein the moving average is calculated as the average of the signal at each cycle with signals at the immediate two earlier and immediate two later cycles. 
     
     
         69 . The method of  claim 65 , wherein the curve is a quadratic curve. 
     
     
         70 . The method of  claim 65 , wherein the multicycle amplification reaction is a 30-50 cycle amplification reaction. 
     
     
         71 . The method of  claim 70 , wherein the multicycle amplification reaction is a 40 cycle amplification reaction. 
     
     
         72 . The method of  claim 65 , wherein the multicycle amplification reaction is quantitative polymerase chain reaction (qPCR). 
     
     
         73 . The method of  claim 65 , wherein the detectable reporter is a fluorophore and the signal is fluorescence. 
     
     
         74 . The method of  claim 65 , wherein each cycle comprises a nucleic acid denaturation step, an annealing/extension step, and a detection step. 
     
     
         75 . The method of  claim 65 , wherein each cycle comprises a nucleic acid denaturation step, an annealing step, an extension step, and a detection step. 
     
     
         76 . The method of  claim 65 , wherein the sample is a biological sample. 
     
     
         77 . The method of  claim 76 , wherein the target nucleic acid is a viral nucleic acid. 
     
     
         78 . The method of  claim 77 , wherein the amount of target nucleic acid present in the sample is proportional to the viral load in the sample. 
     
     
         79 . A method of preparing a target nucleic acids in a biological sample for subsequent analysis, comprising:
 (a) combining the biological sample with a lysis reagent capable of digesting cell membranes and degrading proteins and allowing the lysis reagent to digest cell membranes and degrade proteins to generate a lysate, wherein the biological sample comprises nucleic acid;   (b) combining the lysate with a capture reagent, wherein the capture reagent comprises a nucleic acid probe tethered to a capture moiety;   (c) allowing the nucleic acid probe to hybridize to the nucleic acids of the biological sample to generate a probe-bound nucleic acid solution;   (d) combining the probe-bound nucleic acid with capture-agent-coated magnetic beads;   (e) allowing the capture agent to bind to the capture moiety to generate a bead-captured nucleic acid suspension;   (f) isolating bead-captured nucleic acids within the bead-captured nucleic acid suspension by exposing a portion of the bead-captured nucleic acid suspension to a magnetic field; and   (g) separating the isolated, bead-captured nucleic acids from a liquid portion of the bead-captured nucleic acid suspension.   
     
     
         80 . A method of preparing a target nucleic acids in a biological sample for subsequent analysis, comprising:
 (a) combining the biological sample with a lysis reagent and a capture reagent, wherein the lysis reagent comprises components capable of digesting cell membranes and degrading cellular proteins, wherein the capture reagent comprises a nucleic acid probe tethered to a capture moiety, and wherein the biological sample comprises nucleic acid;   (b) allowing the lysis reagent to digest cell membranes and degrade proteins to generate a lysate;   (c) allowing the nucleic acid probe to hybridize to the nucleic acids of the biological sample to generate a probe-bound nucleic acid solution;   (d) combining the probe-bound nucleic acid with capture-agent-coated magnetic beads;   (e) allowing the capture agent to bind to the capture moiety to generate a bead-captured nucleic acid suspension;   (f) isolating bead-captured nucleic acids within the bead-captured nucleic acid suspension by exposing a portion of the bead-captured nucleic acid suspension to a magnetic field; and   (g) separating the isolated, bead-captured nucleic acids from a liquid portion of the bead-captured nucleic acid suspension.   
     
     
         81 . The method of  claim 79 or 80 , wherein the lysis reagent is a dry lysis reagent, and wherein the dry lysis reagent is resuspended in the biological sample. 
     
     
         82 . The method of  claim 79 or 80 , wherein the lysis reagent is a concentrated liquid lysis reagent, and wherein the concentrated liquid lysis reagent is diluted in the biological sample. 
     
     
         83 . The method of  claim 79 or 80 , wherein the capture reagent is a dry capture reagent, and wherein the dry capture reagent is resuspended in the lysate. 
     
     
         84 . The method of  claim 79 or 80 , wherein the capture reagent is a concentrated liquid capture reagent, and wherein the concentrated liquid capture reagent is diluted in the lysate. 
     
     
         85 . The method of  claim 79 or 80 , wherein the capture-agent-coated magnetic beads are dry and are resuspended in the probe-bound nucleic acid solution. 
     
     
         86 . The method of  claim 79 or 80 , wherein the capture-agent-coated magnetic beads are in a concentrated liquid and are diluted in the probe-bound nucleic acid solution. 
     
     
         87 . The method of  claim 79 or 80 , wherein the method does not comprise a centrifugation step. 
     
     
         88 . The method of  claim 79 or 80 , wherein the method does not comprise a filtration step. 
     
     
         89 . The method of  claim 79 or 80 , wherein the method does not comprise precipitation of nucleic acids. 
     
     
         90 . The method of  claim 79 or 80 , wherein the nucleic acids are not isolated from contaminants within the biological sample in steps (a) through (e). 
     
     
         91 . The method of  claim 79 or 80 , wherein allowing the lysis reagent to digest cell membranes and degrade proteins to generate a lysate comprises mixing of the biological sample and the lysis reagent as the temperature is raised to 90-100° C. 
     
     
         92 . The method of  claim 79 or 80 , wherein the lysis reagent comprises a protease capable of digesting cellular proteins. 
     
     
         93 . The method of  claim 92 , wherein the protease is proteinase K. 
     
     
         94 . The method of  claim 79 or 80 , wherein the lysis reagent comprises a detergent at a concentration sufficient to lyse cells. 
     
     
         95 . The method of  claim 94 , wherein the detergent is SDS. 
     
     
         96 . The method of  claim 79 or 80 , wherein the lysis reagent comprises one or more salts. 
     
     
         97 . The method of  claim 79 or 80 , wherein the capture moiety is biotin and the capture agent is streptavidin. 
     
     
         98 . The method of  claim 79 or 80 , wherein the nucleic acid probe comprises a hybridization sequence that is complementary to a target sequence in the nucleic acids of the biological sample. 
     
     
         99 . The method of  claim 98 , wherein allowing the nucleic acid probe to hybridize to the nucleic acids of the biological sample comprises mixing the lysate and the capture reagent. 
     
     
         100 . The method of  claim 98 , wherein allowing the nucleic acid probe to hybridize to the nucleic acids of the biological sample comprises incubating the lysate and the capture reagent at 63-73° C. 
     
     
         101 . The method of  claim 100 , wherein allowing the nucleic acid probe to hybridize to the nucleic acids of the biological sample comprises incubating the lysate and the capture reagent at about 68° C. 
     
     
         102 . The method of  claim 98 , wherein the lysate and the capture reagent are mixed and/or incubated for 30 seconds to 5 minutes. 
     
     
         103 . The method of  claim 102 , wherein the lysate and the capture reagent are mixed and/or incubated for 1 to 3 minutes. 
     
     
         104 . The method of  claim 103 , wherein the lysate and the capture reagent are incubated for about 2 minutes. 
     
     
         105 . The method of  claim 79 or 80 , wherein combining the probe-bound nucleic acid with the capture-agent-coated magnetic beads comprises mixing the probe-bound nucleic acid and the capture-agent-coated magnetic beads 
     
     
         106 . The method of  claim 79 or 80 , wherein combining the probe-bound nucleic acid with the capture-agent-coated magnetic beads comprises incubating the probe-bound nucleic acid and the capture-agent-coated magnetic beads at 70-80° C. 
     
     
         107 . The method of  claim 106 , wherein combining the probe-bound nucleic acid with the capture-agent-coated magnetic beads comprises incubating the probe-bound nucleic acid and the capture-agent-coated magnetic beads at about 75° C. 
     
     
         108 . The method of  claim 79 or 80 , wherein allowing the capture agent to bind to the capture moiety comprises incubating the probe-bound nucleic acid and the capture-agent-coated magnetic beads at 63-73° C. 
     
     
         109 . The method of  claim 108 , wherein allowing the capture agent to bind to the capture moiety comprises incubating the probe-bound nucleic acid and the capture-agent-coated magnetic beads at about 68° C. 
     
     
         110 . The method of  claim 79 or 80 , further comprising aspirating the bead-captured nucleic acid suspension prior to exposure to the magnetic field 
     
     
         111 . The method of  claim 79 or 80 , wherein separating the isolated, bead-captured nucleic acids and the liquid portion of the bead-captured nucleic acid suspension comprises holding the magnetic field in place and removing the liquid portion from the bead-captured nucleic acid suspension; 
     
     
         112 . The method of  claim 79 or 80 , further comprising:
 (h) combining the isolated bead-captured nucleic acid with a wash buffer;   (i) resuspending the bead-captured nucleic acid in the wash buffer;   (j) isolating the bead-captured nucleic acids within the wash buffer by exposing a portion of the bead-captured nucleic acids to a magnetic field; and   (k) separating the isolated, bead-captured nucleic acids from the wash buffer.   
     
     
         113 . The method of  claim 112 , further comprising repeating steps (h)-(k) one or more times. 
     
     
         114 . The method of  claim 79 or 80 , further comprising:
 (h) combining the isolated bead-captured nucleic acid with a resuspension buffer; and   (i) resuspending the bead-captured nucleic acid in the resuspension buffer to generate a bead-captured nucleic acid resuspension.   
     
     
         115 . The method of  claim 114 , further comprising:
 (j) combining the bead-captured nucleic acid resuspension with analysis reagents.   
     
     
         116 . The method of  claim 112 , further comprising:
 (l) combining the isolated bead-captured nucleic acid with a resuspension buffer; and   (m) resuspending the bead-captured nucleic acid in the resuspension buffer to generate a bead-captured nucleic acid resuspension.   
     
     
         117 . The method of  claim 116 , further comprising:
 (n) combining the bead-captured nucleic acid resuspension with analysis reagents.   
     
     
         118 . The method of  claim 115 or 117 , wherein the analysis reagents are dry analysis reagents and combining the bead-captured nucleic acid resuspension with the dry analysis reagents comprises resuspending the dry analysis reagents in the bead-captured nucleic acid resuspension. 
     
     
         119 . The method of  claim 115 or 117 , wherein the analysis reagents comprise detection reagents. 
     
     
         120 . The method of  claim 115 or 117 , wherein the analysis reagents comprise amplification reagents. 
     
     
         121 . The method of  claim 115 or 117 , further comprising amplifying and/or detecting the target nucleic acid hybridized to the bead-bound capture reagent. 
     
     
         122 . The method of  claim 78 or 80 , wherein the wash buffer and resuspension buffer contain the same components. 
     
     
         123 . A method of preparing a target nucleic acids in a biological sample for subsequent analysis, comprising:
 (a) combining the biological sample comprising cells with a dry lysis reagent comprising proteinase K, SDS, and salt; and resuspending the dry lysis reagent in the biological sample to generate a lysate;   (b) combining the lysate with a dry capture reagent and resuspending the dry capture reagent in the lysate, wherein the capture reagent comprises a nucleic acid probe tethered to a capture moiety, wherein the capture moiety is biotin, and wherein the nucleic acid probe comprises a hybridization sequence that is complementary to a target sequence within the nucleic acids of the biological sample;   (c) incubating the nucleic acid probe and the nucleic acids of the lysate at a temperature of 63-73° C. to generate a probe-bound nucleic acid solution;   (d) combining the probe-bound nucleic acid with dry capture-agent-coated magnetic beads and resuspending the dry capture-agent-coated magnetic beads in the probe-bound nucleic acid at 70-80° C., wherein the capture agent is streptavidin;   (e) incubating the probe-bound nucleic acid and capture-agent-coated magnetic beads at 63-73° C. and allowing the capture agent to bind to the capture moiety to generate a bead-captured nucleic acid suspension;   (f) isolating bead-captured nucleic acids within the bead-captured nucleic acid suspension by exposing a portion of the bead-captured nucleic acid suspension to a magnetic field, and (A) holding the magnetic field in place while removing the liquid portion from the bead-captured nucleic acid suspension, or (B) moving the magnetic field to drag the bead-captured nucleic acids from the liquid portion; and   (g) separating the isolated, bead-captured nucleic acids from a liquid portion of the bead-captured nucleic acid suspension;   (h) combining the isolated bead-captured nucleic acid with a wash buffer;   (i) resuspending the bead-captured nucleic acid in the wash buffer;   (j) isolating the bead-captured nucleic acids within the wash buffer by exposing a portion of the bead-captured nucleic acids to a magnetic field; and   (k) separating the isolated, bead-captured nucleic acids from the wash buffer;   (l) combining the isolated bead-captured nucleic acid with a resuspension buffer; and   (m) resuspending the bead-captured nucleic acid in the resuspension buffer to generate a bead-captured nucleic acid resuspension;   (n) combining the bead-captured nucleic acid resuspension with dry analysis reagents and resuspending the dry analysis reagents in the bead-captured nucleic acid resuspension, wherein the analysis reagents comprise primers and detectable labels for amplifying and detecting the target nucleic acids; and   (o) amplifying and detecting the target nucleic acid hybridized to the bead-bound capture reagent;   wherein the method does not comprise a centrifugation step, a filtration step, or nucleic acid precipitation step; wherein the nucleic acids are not isolated from contaminants within the biological sample in steps (a) through (e); and wherein the wash buffer and resuspension buffer contain the same components.   
     
     
         124 . A method of preparing a target nucleic acids in a biological sample for subsequent analysis, comprising:
 (a) combining the biological sample with a dry reagent comprising lysis/digestion components and capture components, and resuspending the dry reagent in the biological sample, wherein the lysis/digestion components comprise proteinase K, SDS, and salt, wherein the capture components comprise comprises a nucleic acid probe tethered to a capture moiety, wherein the capture moiety is biotin, and wherein the nucleic acid probe comprises a hybridization sequence that is complementary to a target sequence within the nucleic acids of the biological sample   (b) incubating biological sample at a temperature 90-100° C. to allow lysis of cell membranes and digestion of proteins within the sample to generate a lysate;   (c) incubating the lysate at a temperature of 63-73° C. to allow binding of the hybridization sequence of the nucleic acid probe to the target sequence of the nucleic acid of the biological sample to generate a probe-bound nucleic acid solution;   (d) combining the probe-bound nucleic acid with dry capture-agent-coated magnetic beads and resuspending the dry capture-agent-coated magnetic beads in the probe-bound nucleic acid at 70-80° C., wherein the capture agent is streptavidin;   (e) incubating the probe-bound nucleic acid and capture-agent-coated magnetic beads at 63-73° C. and allowing the capture agent to bind to the capture moiety to generate a bead-captured nucleic acid suspension;   (f) isolating bead-captured nucleic acids within the bead-captured nucleic acid suspension by exposing a portion of the bead-captured nucleic acid suspension to a magnetic field, and (A) holding the magnetic field in place while removing the liquid portion from the bead-captured nucleic acid suspension, or (B) moving the magnetic field to drag the bead-captured nucleic acids from the liquid portion; and   (g) separating the isolated, bead-captured nucleic acids from a liquid portion of the bead-captured nucleic acid suspension;   (h) combining the isolated bead-captured nucleic acid with a wash buffer;   (i) resuspending the bead-captured nucleic acid in the wash buffer;   (j) isolating the bead-captured nucleic acids within the wash buffer by exposing a portion of the bead-captured nucleic acids to a magnetic field; and   (k) separating the isolated, bead-captured nucleic acids from the wash buffer; (1) combining the isolated bead-captured nucleic acid with a resuspension buffer; and   (m) resuspending the bead-captured nucleic acid in the resuspension buffer to generate a bead-captured nucleic acid resuspension;   (n) combining the bead-captured nucleic acid resuspension with dry analysis reagents and resuspending the dry analysis reagents in the bead-captured nucleic acid resuspension, wherein the analysis reagents comprise primers and detectable labels for amplifying and detecting the target nucleic acids; and   (o) amplifying and detecting the target nucleic acid hybridized to the bead-bound capture reagent;   wherein the method does not comprise a centrifugation step, a filtration step, or nucleic acid precipitation step; wherein the nucleic acids are not isolated from contaminants within the biological sample in steps (a) through (e); and wherein the wash buffer and resuspension buffer contain the same components.   
     
     
         125 . The method of one of  claims 79-124 , wherein the method is performed manually. 
     
     
         126 . The method of  claim 125 , wherein movement and combining of liquids is conducted by manual pipetting. 
     
     
         127 . The method of one of  claims 79-124 , wherein the method is automated. 
     
     
         128 . The method of  claim 127 , wherein the method steps are performed within a single-use cartridge. 
     
     
         129 . The method of  claim 127 , wherein the single-use cartridge contains all dry and liquid reagents and buffers for performing the method steps of the method. 
     
     
         130 . The method of  claim 128 , wherein the single use cartridge interfaces with an instrument that comprises components for combining and mixing reagents, heating elements, and a magnet. 
     
     
         131 . The method of  claim 127 , wherein the method steps are performed by an automation instrument within one or more tubes or wells. 
     
     
         132 . A system or kit comprising:
 (a) a lysis reagent capable of digesting cell membranes and degrading cellular proteins;   (b) a capture reagent comprising a nucleic acid probe tethered to a capture moiety;   (c) capture-agent-coated magnetic beads;   (d) amplification/detection reagents; and   (e) a wash/resuspension buffer solution.   
     
     
         133 . A system or kit comprising:
 (a) a lysis/capture reagent comprising (1) lysis/digestion components capable of digesting cell membranes and degrading proteins, and (2) a nucleic acid probe tethered to a capture moiety;   (b capture-agent-coated magnetic beads;   (c) amplification/detection reagents; and   (d) a wash/resuspension buffer solution.   
     
     
         134 . The system or kit of  claim 132 or 133 , wherein the regents are in a dry or concentrated liquid form. 
     
     
         135 . The system or kit of  claim 132 or 133 , further comprising a biological sample comprising cells. 
     
     
         136 . The system or kit of  claim 132 or 133 , wherein the lysis reagent or lysis/digestion components comprises a protease capable of digesting cellular proteins. 
     
     
         137 . The system or kit of  claim 136 , wherein the protease is proteinase K. 
     
     
         138 . The system or kit of  claim 132 or 133 , wherein the lysis reagent or lysis/digestion components comprises a detergent in an amount sufficient to lyse cells when combined with a biological sample. 
     
     
         139 . The system or kit of  claim 138 , wherein the detergent is SDS. 
     
     
         140 . The system or kit of  claim 132 or 133 , wherein the lysis reagent or lysis/digestion components comprises one or more salts. 
     
     
         141 . The system or kit of  claim 132 or 133 , wherein the capture moiety is biotin and the capture agent is streptavidin. 
     
     
         142 . The system or kit of  claim 132 or 133 , wherein the nucleic acid probe comprises a hybridization sequence that is complementary to a target sequence in a target nucleic acid. 
     
     
         143 . The system or kit of  claim 132 or 133 , wherein the dry amplification/detection reagents comprises primers, detectable labels, and nucleotides. 
     
     
         144 . A system or kit comprising:
 (a) a lysis reagent comprising proteinase K, SDS, and one or more salts;   (b) a capture reagent comprising a nucleic acid probe tethered to a biotin capture moiety;   (c) capture-agent-coated magnetic beads, wherein the capture agent is streptavidin;   (d) amplification/detection reagents comprising primers, detectable labels, and nucleotides; and   (e) a buffer solution.   
     
     
         145 . A system or kit comprising:
 (a) a lysis/capture reagent comprising (1) lysis/digestion components comprising proteinase K, SDS, and one or more salts, and (2) a nucleic acid probe tethered to a capture moiety;   (b) capture-agent-coated magnetic beads, wherein the capture agent is streptavidin;   (c) amplification/detection reagents comprising primers, detectable labels, and nucleotides; and   (d) a buffer solution.   
     
     
         146 . The system or kit of  claim 144 or 145 , wherein the regents are in a dry or concentrated liquid form. 
     
     
         147 . The system or kit of  claim 144 or 145 , further comprising a biological sample comprising cells. 
     
     
         148 . The system or kit of  claim 132, 133, 144 or 145 , further comprising disposable laboratory products for manually using the system or kit for the capture, isolation, amplification, and detection of a target nucleic acid from a biological sample comprising cells. 
     
     
         149 . The system or kit of  claim 148 , wherein the disposable laboratory products comprise pipette tips, reaction tubes, and or a microwell plate. 
     
     
         150 . The system or kit of  claim 149 , further comprising a single-use cartridge containing the components of (a)-(e), wherein the single-use cartridge is capable of interfacing with an instrument that comprises components for combining and mixing reagents, heating elements, and a magnet.